My thoughts in random order:
* If I was starting from scratch I'd run johnny joints on my uppers and lowers. I run 2" x .250" lowers and they have taken a bend after a couple years but I just keep running them. I could see going cromo with them if that's going to bother you but it's not strictly required on a rig under 3500 lbs (according to me). I currently run 3/4" heims on my uppers but after you buy the jam nuts, misalignment spacers, etc. you don't save any money. Also, if you buy pre-fab brackets everything is the world comes in 2 5/8" for johnny joints, jimmy joints, evolution joints, etc. For 3/4" heims you have to set the width yourself.
* It would be nice to avoid the custom fuel cell if you could. It just seems like metal fuel cells have issues with cracking, leaking, etc. and being one of a kind would stink. I'd guess you'll want about 12 gallons with that motor.
* I'm happy not to have a rear suckdown winch. So far my rear limit strap has made me happy and it was nearly free, weighs a few ounces, and it has no packaging issues.
* I've been told that supermarket butchers throw away their giant cutting boards every month or so. I wonder if that could be a source for skid plate material?
* This steering wheel disconnect has always worked for me. If it melted today I'd just get the same thing again. I use mine a lot because I can't really get in or out with the steering wheel attached.
* Consider tool storage early on in the project. Unless you only go to places where you wheel right by the tow rig (gray rock, crozet, DPG, etc.) you'll want to have your tools with you. Also, you need a place for the tree saver/tow strap.
* I think corbeau seats are the best buy out there. After sitting in mastercraft, PRP, Hunsucker, Beard, and corbeau seats I decided that only corbeau and PRPs "hugged" my sides enough. After seeing both PRP and corbeau seats wears for a few years I'm not convinced there is much of a quality difference at all.
* If I was starting from scratch I'd make sure the radiator wasn't right next to the seats. I do like the warm air sometimes (and I just reverse the fan for summer) but the noise is a pita.
Hopefully something in there had some value. 
